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Riffle construction is a common practice in river engineering, but insufficient science exists to guide objective design of riffle-pool relief and the three-dimensional forms of features smaller than the scale of channel width. In this study, numerical experimentation with two-dimensional hydrodynamic modeling and ecohydraulic analysis was used to evaluate the performance of six different configurations of a sequence of riffle-pool units typical of shallow, regulated gravel-bed rivers, emphasizing a range of slope-detrended riffle-pool amplitudes. Two configurations used a high riffle-pool amplitude, three used a low one, and one had an intermediate value with hybrid features. In the experimental design, sixteen specific physical habitat performance indicators and six sediment-transport regime performance indicators were used to compare the design alternatives. Results found that the low riffle-pool relief configurations yielded the best performance for the majority of physical habitat indicators and all of the sediment transport regime indicators. The spatial patterns of test metrics, such as habitat indices and Shields stress revealed the mechanisms responsible for the statistical outcomes. Methodologically, two dimensional modeling and ecohydraulic analysis are vital tools in project design along with previously accepted hydrologic, geomorphic, and engineering analyses. Scientifically, low-relief riffle-pool units are indicated as the normative condition in gravel-bed rivers where forcing elements driving deep scour are not systematically controlling morphology.